Evolutionary lottery of skull and beak morphology
gif provided by the awesome Jen Bright @MorphobeakGeek!
In this exercise we will use a github repo to collaboratively collate and simulate evolutionary trajectories for each participants’ species body size using a simple brownian motion evolutionary model. This assumes evolutionary steps to progress comletely at random. You could say:
it’s a bit of lottery!
Each participant has created and contributed a file specifying the parameters required to simulate and plot their species evolutionary trajectory. We’ve collect all participants’ files in the master repo. Next we need to simulate species trajectories plot them up.
Participants will then get to see the skull and beak shape corresponding to their species relative body size!
setup
First we load the required packages and create some objects to compile data on trait evolution for each species.
require(dplyr)
require(ggplot2)
require(plotly)
set.seed(1)
t <- 0:100 # generate time vector
dt <- NULL # generate object to compile time-series data
cols <- NULL # generate object to compile trendline coloursSimulate trait evolution, iterate over all species files in params/ folder
We’ll use the parameters supplied in your scripts to generate brownian trait evolution trendline for each species.
spp.files <- dir("params/")[dir("params/") != "params_tmpl.R"]
for(spp in spp.files){
# source parameters for each species
source(file.path("params", spp))
# generate trait evolution time-series and compile plotting data
dt <- rbind(dt, data.frame(t,
trait = c(0, rnorm(n = length(t) - 1, sd = sqrt(sig2)) %>% cumsum()),
species = species.name))
cols <- c(cols, color)
}Plot trait evolution timeseries
Use the data generated to plot all species.
p <- ggplot(data = dt, aes(x = t, y = trait, group = species, colour = species)) +
geom_line() +
scale_colour_manual(values = cols)
ggplotly(p)Skulls! find the skull associated with your species:
Skulls are organised from largest to smallest. The largest skulls are vulture-like, (e.g. no. 50, the Andean condor Vultur gryphus) and the smallest are falconet-like, (e.g. no. 1 Collared falconet Microhierax caerulescens)
No: 47 marco_pigeons
No: 44 lewisus_beakmaximii
No: 42 Lucius_wilvus
No: 40 nighthawk_stuartbroad
No: 39 amberus_landy
No: 32 mattus_smithii
No: 31 carlus_suligoii
No: 31 big_bird
No: 27 Remyus_venerus
No: 22 Carrot catticus
No: 22 melissa_shawbird
No: 20 happy_alien
No: 19 Amy Smallshaw
No: 14 davidus_wilbyii
No: 7 owl_futuramii
No: 2 sillius_parrotus
Session Info
sessioninfo::session_info()## ─ Session info ───────────────────────────────────────────────────────────────
## setting value
## version R version 4.1.2 (2021-11-01)
## os Ubuntu 18.04.6 LTS
## system x86_64, linux-gnu
## ui X11
## language en_GB:en
## collate en_GB.UTF-8
## ctype en_GB.UTF-8
## tz Europe/London
## date 2022-07-26
##
## ─ Packages ───────────────────────────────────────────────────────────────────
## ! package * version date lib source
## bslib 0.3.1 2021-10-06 [1] CRAN (R 4.1.2)
## cli 3.1.0 2021-10-27 [1] CRAN (R 4.1.2)
## colorspace 2.0-2 2021-06-24 [1] CRAN (R 4.1.2)
## crayon 1.4.2 2021-10-29 [1] CRAN (R 4.1.2)
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## P yaml 2.2.1 2020-02-01 [?] CRAN (R 4.1.1)
##
## [1] /home/ac1dwi/RSE-Sheffield/collaborative_github_exercise/renv/library/R-4.1/x86_64-pc-linux-gnu
## [2] /tmp/RtmpEozPZm/renv-system-library
##
## P ── Loaded and on-disk path mismatch.This projects uses renv for dependency management.